I am working on two populations of invasive and non-invasive bacterial samples. I have found hundreds of genes that are present only in invasive samples. The sequence and annotation of all genes are available. I want to investigate the pathways that these genes are involved. What tools do you suggest?

However, keep in mind that most of the online tools are tuned for human, or mice and rat, so it may complicate your task. If the tool allows (such as webgestalt mentioned earlier) I would suggest using background (reference) genes list at least.